Population-level approaches reveal novel aspects of lignin biosynthesis, content, composition and structure

Computational study on the impact of linkage sequence on the structure and dynamics of lignin

Lignin, one of the most abundant biopolymers on Earth, is of great research interest due to its industrial applications including biofuel production and materials science. The structural composition of lignin plays an important role in shaping its properties and functionalities. Notably, lignin exhibits substantial compositional diversity, which varies not only between different plant species but even within the same plant. Currently, it is unclear to what extent this compositional diversity plays on the overall structure and dynamics of lignin. To address this question, this paper reports on the development of two models of lignin containing all guaiacyl (G) subunits with varied linkage sequences and makes use of all-atom molecular dynamics simulations to examine the impact of linkage sequence alone on the lignin's structure and dynamics. This work demonstrates that the structure of the lignin polymer depends on its linkage sequence at temperatures above and below the glass transition temperature ( T g ), but the polymers exhibit similar structural properties as it is approaching the viscous flow state (480 K). At low temperatures, both of lignin models have a local dynamics confined in a cage, but the size of cages varies depending on structural differences. Interestingly, at temperatures higher than T g , the different linkage sequence leads to the subtle dynamical difference which diminishes at 480 K.

Enabling Lignin Valorization Through Integrated Advances in Plant Biology and Biorefining

Despite lignin having long been viewed as an impediment to the processing of biomass for the production of paper, biofuels, and high-value chemicals, the valorization of lignin to fuels, chemicals, and materials is now clearly recognized as a critical element for the lignocellulosic bioeconomy. However, the intended application for lignin will likely require a preferred lignin composition and form. To that end, effective lignin valorization will require the integration of plant biology, providing optimal feedstocks, with chemical process engineering, providing efficient lignin transformations. Recent advances in our understanding of lignin biosynthesis have shown that lignin structure is extremely diverse and potentially tunable, while simultaneous developments in lignin refining have resulted in the development of several processes that are more agnostic to lignin composition. Here, we review the interface between in planta lignin design and lignin processing and discuss the advances necessary for lignin valorization to become a feature of advanced biorefining.

Design and Validation of a High-Throughput Reductive Catalytic Fractionation Method

Reductive catalytic fractionation (RCF) is a promising method to extract and depolymerize lignin from biomass, and bench-scale studies have enabled considerable progress in the past decade. RCF experiments are typically conducted in pressurized batch reactors with volumes ranging between 50 and 1000 mL, limiting the throughput of these experiments to one to six reactions per day for an individual researcher. Here, we report a high-throughput RCF (HTP-RCF) method in which batch RCF reactions are conducted in 1 mL wells machined directly into Hastelloy reactor plates. The plate reactors can seal high pressures produced by organic solvents by vertically stacking multiple reactor plates, leading to a compact and modular system capable of performing 240 reactions per experiment. Using this setup, we screened solvent mixtures and catalyst loadings for hydrogen-free RCF using 50 mg poplar and 0.5 mL reaction solvent. The system of 1:1 isopropanol/methanol showed optimal monomer yields and selectivity to 4-propyl substituted monomers, and validation reactions using 75 mL batch reactors produced identical monomer yields. To accommodate the low material loadings, we then developed a workup procedure for parallel filtration, washing, and drying of samples and a 1H nuclear magnetic resonance spectroscopy method to measure the RCF oil yield without performing liquid-liquid extraction. As a demonstration of this experimental pipeline, 50 unique switchgrass samples were screened in RCF reactions in the HTP-RCF system, revealing a wide range of monomer yields (21-36%), S/G ratios (0.41-0.93), and oil yields (40-75%). These results were successfully validated by repeating RCF reactions in 75 mL batch reactors for a subset of samples. We anticipate that this approach can be used to rapidly screen substrates, catalysts, and reaction conditions in high-pressure batch reactions with higher throughput than standard batch reactors.

Review of the application of bimetallic catalysts coupled with internal hydrogen donor for catalytic hydrogenolysis of lignin to produce phenolic fine chemicals

Lignocellulosic biomass contains lignin, an aromatic and oxygenated substance and a potential method for lignin utilization is achieved through catalytic conversion into useful phenolic and aromatic monomers. The application of monometallic catalysts for lignin hydrogenolysis reaction remains one of the major reasons for the underutilization of lignin to produce valuable chemicals. Monometallic catalysts have many limitations such as limited catalytic sites for interacting with different lignin linkages, poor catalytic activity, low lignin conversion, and low product selectivity. It is due to lack of synergy with other metallic catalysts that can enhance the catalytic activity, stability, selectivity, and overall catalytic performance. To overcome these limitations, works on the application of bimetallic catalysts that can offer higher activity, selectivity, and stability have been initiated. In this review, cutting-edge insights into the catalytic hydrogenolysis of lignin, focusing on the production of phenolic and aromatic monomers using bimetallic catalysts within an internal hydrogen donor solvent are discussed. The contribution of this work lies in a critical discussion of recent reported findings, in-depth analyses of reaction mechanisms, optimal conditions, and emerging trends in lignin catalytic hydrogenolysis. The specific effects of catalytic active components on the reaction outcomes are also explored. Additionally, this review extends beyond current knowledge, offering forward-looking suggestions for utilizing lignin as a raw material in the production of valuable products across various industrial processes. This work not only consolidates existing knowledge but also introduces novel perspectives, paving the way for future advancements in lignin utilization and catalytic processes.

Genetic markers and tree properties predicting wood biorefining potential in aspen (Populus tremula) bioenergy feedstock

BACKGROUND

Wood represents the majority of the biomass on land and constitutes a renewable source of biofuels and other bioproducts. However, wood is recalcitrant to bioconversion, raising a need for feedstock improvement in production of, for instance, biofuels. We investigated the properties of wood that affect bioconversion, as well as the underlying genetics, to help identify superior tree feedstocks for biorefining.

RESULTS

We recorded 65 wood-related and growth traits in a population of 113 natural aspen genotypes from Sweden ( https://doi.org/10.5061/dryad.gtht76hrd ). These traits included three growth and field performance traits, 20 traits for wood chemical composition, 17 traits for wood anatomy and structure, and 25 wood saccharification traits as indicators of bioconversion potential. Glucose release after saccharification with acidic pretreatment correlated positively with tree stem height and diameter and the carbohydrate content of the wood, and negatively with the content of lignin and the hemicellulose sugar units. Most of these traits displayed extensive natural variation within the aspen population and high broad-sense heritability, supporting their potential in genetic improvement of feedstocks towards improved bioconversion. Finally, a genome-wide association study (GWAS) revealed 13 genetic loci for saccharification yield (on a whole-tree-biomass basis), with six of them intersecting with associations for either height or stem diameter of the trees.

CONCLUSIONS

The simple growth traits of stem height and diameter were identified as good predictors of wood saccharification yield in aspen trees. GWAS elucidated the underlying genetics, revealing putative genetic markers for bioconversion of bioenergy tree feedstocks.

Combined Transcriptome and Metabolome Analyses Reveal Candidate Genes Involved in Tangor (Citrus reticulata × Citrus sinensis) Fruit Development and Quality Formation

Tangor, an important citrus type, is a hybrid of orange and mandarin and possesses their advantageous characteristics. Fruit quality is an important factor limiting the development of the citrus industry and highly depends on fruit development and ripening programs. However, fruit development and quality formation have not been completely explored in mandarin-orange hybrids. We sequenced the metabolome and transcriptome of three mandarin-orange hybrid cultivars at the early fruiting [90 days after full bloom (DAFB)], color change (180 DAFB), and ripening (270 DAFB) stages. Metabolome sequencing was performed to preliminarily identify the accumulation patterns of primary and secondary metabolites related to fruit quality and hormones regulating fruit development. Transcriptome analysis showed that many genes related to primary metabolism, secondary metabolism, cell wall metabolism, phytohormones, and transcriptional regulation were up-regulated in all three cultivars during fruit development and ripening. Additionally, multiple key genes were identified that may play a role in sucrose, citric acid and flavonoid accumulation, cell wall modification, and abscisic acid signaling, which may provide a valuable resource for future research on enhancement of fruit quality of hybrid citrus. Overall, this study provides new insights into the molecular basis of pulp growth and development regulation and fruit quality formation in mandarin-orange hybrids.

Microbial assimilation of lignin-derived aromatic compounds and conversion to value-added products

Lignin is an abundant and sustainable source of aromatic compounds that can be converted to value-added products. However, lignin is underutilized, since depolymerization produces a complex mixture of aromatic compounds that is difficult to convert to a single product. Microbial conversion of mixed aromatic substrates provides a potential solution to this conversion challenge. Recent advances have expanded the range of lignin-derived aromatic substrates that can be assimilated and demonstrated efficient conversion via central metabolism to new potential products. The development of additional non-model microbial hosts and genetic tools for these hosts have accelerated engineering efforts. However, yields with real depolymerized lignin are still low, and additional work will be required to achieve viable conversion processes.

Genomic and transcriptomic analyses of Citrus sinensis varieties provide insights into Valencia orange fruit mastication trait formation

Valencia orange (Citrus sinensis Osbeck) (VO) is a type of late-ripening sweet orange whose ripening occurs 4 to 5 months later than that of the mid-ripening common sweet orange (CO). Notably, the mastication trait of VO fruit is inferior to that of CO fruit. To date, how inferior pulp mastication trait forms in VO has not been determined. In this study, 13 VO varieties and 12 CO varieties were subjected to whole-genome resequencing. A total of 2.98 million SNPs were identified from 25 varieties, and a SNP molecular marker was developed to distinguish VO and CO. Moreover, 144 and 141 genes identified by selective sweep analysis were selected during VO and CO evolution, respectively. Based on gene functional enrichment analysis, most of the selected VO genes were related to the stress response and lignin biosynthesis. Simultaneously, we comparatively analyzed the transcriptome profiles of peel and pulp tissues among three VO varieties and three CO varieties, and the results demonstrated differences in lignin biosynthesis between VO and CO fruits. Furthermore, coexpression network analysis was performed to identify hub genes of lignin-related and variety-specific networks, which included CsERF74, CsNAC25, CsHSFB3, CsSPL4/13, etc. Overall, this study provides important insights into the mastication trait formation of Valencia orange fruit.

Accurate determination of genotypic variance of cell wall characteristics of a Populus trichocarpa pedigree using high-throughput pyrolysis-molecular beam mass spectrometry

BACKGROUND

Pyrolysis-molecular beam mass spectrometry (py-MBMS) analysis of a pedigree of Populus trichocarpa was performed to study the phenotypic plasticity and heritability of lignin content and lignin monomer composition. Instrumental and microspatial environmental variability were observed in the spectral features and corrected to reveal underlying genetic variance of biomass composition.

RESULTS

Lignin-derived ions (including m/z 124, 154, 168, 194, 210 and others) were highly impacted by microspatial environmental variation which demonstrates phenotypic plasticity of lignin composition in Populus trichocarpa biomass. Broad-sense heritability of lignin composition after correcting for microspatial and instrumental variation was determined to be H² = 0.56 based on py-MBMS ions known to derive from lignin. Heritability of lignin monomeric syringyl/guaiacyl ratio (S/G) was H² = 0.81. Broad-sense heritability was also high (up to H² = 0.79) for ions derived from other components of the biomass including phenolics (e.g., salicylates) and C5 sugars (e.g., xylose). Lignin and phenolic ion abundances were primarily driven by maternal effects, and paternal effects were either similar or stronger for the most heritable carbohydrate-derived ions.

CONCLUSIONS

We have shown that many biopolymer-derived ions from py-MBMS show substantial phenotypic plasticity in response to microenvironmental variation in plantations. Nevertheless, broad-sense heritability for biomass composition can be quite high after correcting for spatial environmental variation. This work outlines the importance in accounting for instrumental and microspatial environmental variation in biomass composition data for applications in heritability measurements and genomic selection for breeding poplar for renewable fuels and materials.

Recent Advances in the Catalytic Depolymerization of Lignin towards Phenolic Chemicals: A Review

The efficient valorization of lignin could dictate the success of the 2nd generation biorefinery. Lignin, accounting for on average a third of the lignocellulosic biomass, is the most promising candidate for sustainable production of value-added phenolics. However, the structural alteration induced during lignin isolation is often depleting its potential for value-added chemicals. Recently, catalytic reductive depolymerization of lignin has appeared to be a promising and effective method for its valorization to obtain phenolic monomers. The present study systematically summarizes the far-reaching and state-of-the-art lignin valorization strategies during different stages, including conventional catalytic depolymerization of technical lignin, emerging reductive catalytic fractionation of protolignin, stabilization strategies to inhibit the undesired condensation reactions, and further catalytic upgrading of lignin-derived monomers. Finally, the potential challenges for the future researches on the efficient valorization of lignin and possible solutions are proposed.

Mesoscale Reaction-Diffusion Phenomena Governing Lignin-First Biomass Fractionation

Lignin solvolysis from the plant cell wall is the critical first step in lignin depolymerization processes involving whole biomass feedstocks. However, little is known about the coupled reaction kinetics and transport phenomena that govern the effective rates of lignin extraction. Here, we report a validated simulation framework that determines intrinsic, transport-independent kinetic parameters for the solvolysis of lignin, hemicellulose, and cellulose upon incorporation of feedstock characteristics for the methanol-based extraction of poplar as an example fractionation process. Lignin fragment diffusion is predicted to compete on the same time and length scales as reactions of lignin within cell walls and longitudinal pores of typical milled particle sizes, and mass transfer resistances are predicted to dominate the solvolysis of poplar particles that exceed approximately 2 mm in length. Beyond the approximately 2 mm threshold, effectiveness factors are predicted to be below 0.25, which implies that pore diffusion resistances may attenuate observable kinetic rate measurements by at least 75 % in such cases. Thus, researchers are recommended to conduct kinetic evaluations of lignin-first catalysts using biomass particles smaller than approximately 0.2 mm in length to avoid feedstock-specific mass transfer limitations in lignin conversion studies. Overall, this work highlights opportunities to improve lignin solvolysis by genetic engineering and provides actionable kinetic information to guide the design and scale-up of emerging biorefinery strategies.

Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in Populus deltoides

Despite the growing resources and tools for high-throughput characterization and analysis of genomic information, the discovery of the genetic elements that regulate complex traits remains a challenge. Systems genetics is an emerging field that aims to understand the flow of biological information that underlies complex traits from genotype to phenotype. In this study, we used a systems genetics approach to identify and evaluate regulators of the lignin biosynthesis pathway in Populus deltoides by combining genome, transcriptome, and phenotype data from a population of 268 unrelated individuals of P. deltoides The discovery of lignin regulators began with the quantitative genetic analysis of the xylem transcriptome and resulted in the detection of 6706 and 4628 significant local- and distant-eQTL associations, respectively. Among the locally regulated genes, we identified the R2R3-MYB transcription factor MYB125 (Potri.003G114100) as a putative trans-regulator of the majority of genes in the lignin biosynthesis pathway. The expression of MYB125 in a diverse population positively correlated with lignin content. Furthermore, overexpression of MYB125 in transgenic poplar resulted in increased lignin content, as well as altered expression of genes in the lignin biosynthesis pathway. Altogether, our findings indicate that MYB125 is involved in the control of a transcriptional coexpression network of lignin biosynthesis genes during secondary cell wall formation in P. deltoides.